Agent skill · research science · google-deepmind
protein-sequence-msa
Performs multiple sequence alignment of proteins with EBI Clustal Omega. Use when you need to align multiple sequences to assess similarity, domain conservation, or key residue conservation. Supports up to 4000 sequences and a maximum file size of 4 MB. Do not use to search for homologous proteins in a database (use MMseqs2, BLAST), align non-protein sequences (DNA, RNA), perform structural alignment (use Foldseek, PyMOL), or if you only have a single sequence.
Why this skill is useful
Provides specific commands and procedures for using EBI Clustal Omega for protein sequence alignment that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 3k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/proteinsequencemsaLICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.ebi.ac.uk/jdispatcher/msa/clustalo and https://www.ebi.ac.uk/about/terms-of-use/, then (2) create the file recording the notification text and timestamp. 3. .env file: Make sure the .env file exists in your home directory. Create one if it does not exist. 4. USEREMAIL: Required by the wrapper script for Clustal Omega job tracking (recommended by the EBI). You MUST use the safe credentials protocol in the credentials skill to check for and request this credential if this skill looks relevant to the user's request. Core Rules Use the Wrapper: ALWAYS execute the alignment using scripts/msaalign.py rather than writing your own curl or custom Python requests. The script automatically enforces the required rate limit to respect EBI's Terms of Use. Notification: If this skill is used, ensure this is mentioned in the output. Always state the method: Every report must clearly state that the alignment was performed using EBI Clustal Omega. No Hallucinations: Do NOT invent alignments or conservation metrics. Report only what is present in the alignment file. Goal Take a file containing multiple protein sequences in FASTA format, perform multiple sequence alignment using the EBI Clustal Omega API, save the resulting alignment locally for future programmatic analysis, and interpret the results towards addressing the user's specific research objective (e.g., assessing similarity, identifying conserved domains, or analyzing key residues). Instructions 1. Prepare Input File: The input must be a plain text file containing two or more protein sequences in FASTA format. Each sequence header must start with a > symbol. Example: 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/protein_sequence_msa